GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Burkholderia phytofirmans PsJN

Align UDP-glucose 4-epimerase (EC 5.1.3.7; EC 5.1.3.2) (characterized)
to candidate BPHYT_RS04450 BPHYT_RS04450 UDP-glucose 4-epimerase

Query= metacyc::BSU38860-MONOMER
         (339 letters)



>FitnessBrowser__BFirm:BPHYT_RS04450
          Length = 340

 Score =  448 bits (1153), Expect = e-131
 Identities = 215/333 (64%), Positives = 258/333 (77%)

Query: 3   ILVTGGAGYIGSHTCVELLNSGYEIVVLDNLSNSSAEALNRVKEITGKDLTFYEADLLDR 62
           ILVTGGAG+IGSHTCVELLN GY++VV+DNL NS+ E+L RV++ITGK +TFYEAD  D 
Sbjct: 7   ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVNSNRESLRRVEKITGKAVTFYEADARDE 66

Query: 63  EAVDSVFAENEIEAVIHFAGLKAVGESVAIPLKYYHNNLTGTFILCEAMEKYGVKKIVFS 122
            A++ +F  + I   IHFA LKAVGESVA P++YY NN+     L   M    VK+ VFS
Sbjct: 67  AALNRIFDAHPITGAIHFAALKAVGESVAKPIEYYSNNVGSLLTLLGVMRDRNVKQFVFS 126

Query: 123 SSATVYGVPETSPITEDFPLGATNPYGQTKLMLEQILRDLHTADNEWSVALLRYFNPFGA 182
           SSATVYGVP++SPI E FPL ATNPYGQ+KL+ EQ+LRDL  AD  W +A LRYFNP GA
Sbjct: 127 SSATVYGVPKSSPIDESFPLSATNPYGQSKLIAEQVLRDLELADPSWRIATLRYFNPVGA 186

Query: 183 HPSGRIGEDPNGIPNNLMPYVAQVAVGKLEQLSVFGNDYPTKDGTGVRDYIHVVDLAEGH 242
           H SG IGEDP GIPNNLMPYVAQVAVGKLE+L VFG DY T DGTGVRDYIHVVDLA GH
Sbjct: 187 HESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGGDYETPDGTGVRDYIHVVDLARGH 246

Query: 243 VKALEKVLNSTGADAYNLGTGTGYSVLEMVKAFEKVSGKEVPYRFADRRPGDIATCFADP 302
           + AL+ ++    +   NLGTG GYSV+++VKAFEK +G+ VPY    RRPGD+A+CFADP
Sbjct: 247 LAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKAAGRPVPYEIVARRPGDVASCFADP 306

Query: 303 AKAKRELGWEAKRGLEEMCADSWRWQSSNVNGY 335
           A A++ +GW A+ G+E MCAD WRWQS+N  G+
Sbjct: 307 AAAEKIIGWRAQFGIERMCADHWRWQSTNPQGF 339


Lambda     K      H
   0.315    0.134    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 443
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 339
Length of database: 340
Length adjustment: 28
Effective length of query: 311
Effective length of database: 312
Effective search space:    97032
Effective search space used:    97032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS04450 BPHYT_RS04450 (UDP-glucose 4-epimerase)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01179.hmm
# target sequence database:        /tmp/gapView.18328.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.8e-137  442.9   0.0   3.2e-137  442.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS04450  BPHYT_RS04450 UDP-glucose 4-epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS04450  BPHYT_RS04450 UDP-glucose 4-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.8   0.0  3.2e-137  3.2e-137       2     331 ..       7     338 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.8 bits;  conditional E-value: 3.2e-137
                                TIGR01179   2 iLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleee 69 
                                              iLvtGgaG+iGsh++++ll+ g++vvv+Dnl+++++e+l+++ekit  +v+++e+d +d+++l+++++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS04450   7 ILVTGGAGFIGSHTCVELLNGGYDVVVIDNLVNSNRESLRRVEKITgkAVTFYEADARDEAALNRIFDAH 76 
                                              9********************************************9999********************* PP

                                TIGR01179  70 kidaviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespl 139
                                               i   iHfaal+avgEsv++P++YY+nnv + l+Ll +m++ +vk+++Fsssa+vYg ++++pi E++pl
  lcl|FitnessBrowser__BFirm:BPHYT_RS04450  77 PITGAIHFAALKAVGESVAKPIEYYSNNVGSLLTLLGVMRDRNVKQFVFSSSATVYGVPKSSPIDESFPL 146
                                              ********************************************************************** PP

                                TIGR01179 140 npinpYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkre 208
                                              +++npYG+skl++E++l+dl+ ad++++++ LRYFn++GA+e+g iGe++ +++ +l+++va+vavgk+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS04450 147 SATNPYGQSKLIAEQVLRDLELADPSWRIATLRYFNPVGAHESGLIGEDPAGIPnNLMPYVAQVAVGKLE 216
                                              ******************************************************9*************** PP

                                TIGR01179 209 kleifGtdyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkd 278
                                              kl++fG+dy+t+DGt+vRDyiHv Dla +Hlaal+al + + s v nlG+gqg+sv +v++a++k++g++
  lcl|FitnessBrowser__BFirm:BPHYT_RS04450 217 KLRVFGGDYETPDGTGVRDYIHVVDLARGHLAALDALVKRDASFVVNLGTGQGYSVIDVVKAFEKAAGRP 286
                                              ********************************************************************** PP

                                TIGR01179 279 ikveladrRaGDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                              +++e+ +rR+GD+as++ad++ +++ +gw+++++ +e ++++ w+W++++++g
  lcl|FitnessBrowser__BFirm:BPHYT_RS04450 287 VPYEIVARRPGDVASCFADPAAAEKIIGWRAQFG-IERMCADHWRWQSTNPQG 338
                                              **********************************.*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (340 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.45
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory